Buggy code:
public void findAllOverlappingTfbsIntervalsWithNumbers ( String outputFolder , WriteElementBasedAnnotationFoundOverlapsMode writeElementBasedAnnotationFoundOverlapsMode , IntervalTreeNode node , Interval interval , ChromosomeName chromName , TIntByteMap tfNumberCellLineNumber2ZeroorOneMap , List < TfCellLineOverlapWithNumbers > tfandCellLineOverlapList , int overlapDefinition , TShortObjectMap < String > tfNumber2TfNameMap , TShortObjectMap < String > cellLineNumber2CellLineNameMap , TShortObjectMap < String > fileNumber2FileNameMap ) { } public void findAllOverlappingTfbsIntervals ( String outputFolder , IntervalTreeNode node , Interval interval , ChromosomeName chromName , Map < String , BufferedWriter > bufferedWriterHashMap , List < String > tfbsNameList , Map < String , Integer > tfbsNameandCellLineName2ZeroorOneMap , List < TfNameandCellLineNameOverlap > tfandCellLineOverlapList , int overlapDefinition ) { } public void findAllOverlappingTfbsIntervals ( IntervalTreeNode node , Interval interval , BufferedWriter bufferedWriter , List < IntervalTreeNode > overlappedNodeList ) { } public void findAllOverlappingDnaseIntervals ( IntervalTreeNode node , Interval interval , BufferedWriter bufferedWriter , List < IntervalTreeNode > overlappedNodeList ) { } public void findAllOverlappingDnaseIntervalsWithIOWithNumbers ( String outputFolder , int permutationNumber , IntervalTreeNode node , InputLineMinimal interval , ChromosomeName chromName , TIntObjectMap < BufferedWriter > bufferedWriterHashMap , TIntByteMap dnaseCellLineNumber2PermutationZeroorOneMap , int overlapDefinition ) { } public void findAllOverlappingDnaseIntervalsWithIOWithNumbers ( String outputFolder , int permutationNumber , IntervalTreeNode node , InputLineMinimal interval , ChromosomeName chromName , TIntObjectMap < BufferedWriter > bufferedWriterHashMap , TIntIntMap permutationNumberDnaseCellLineNumber2ZeroorOneMap , int overlapDefinition ) { } public static int getGeneSetNumber ( long permutationNumberElementNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getCellLineNumberOrGeneSetNumber ( int permutationNumberCellLineNumberOrKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int removeCellLineNumber ( int elementNumberCellLineNumberKeggPathwayNumber ) { } public static int removeElementNumberCellLineNumber ( int elementNumberCellLineNumberKeggPathwayNumber ) { } public static int removeCellLineNumberKeggPathwayNumber ( int elementNumberCellLineNumberKeggPathwayNumber ) { } public static int getKeggPathwayNumber ( long elementNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static short getKeggPathwayNumber ( int elementNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static short getCellLineNumber ( int mixedNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getCellLineNumber ( long mixedNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static short getShortElementNumber ( int mixedNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getElementTypeNumber ( long mixedNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getElementTypeNumber ( int elementTypeNumberElementNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getElementNumber ( int elementTypeNumberElementNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getElementNumber ( long mixedNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getPermutationNumberRemovedMixedNumber ( long permutationNumberTforHistoneNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long getPermutationNumberRemovedLongMixedNumber ( long permutationNumberElementNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getPermutationNumber ( int permutationNumberCellLineNumberOrGeneSetNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int getPermutationNumber ( long permutationNumberElementNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long generatePermutationNumberGeneNumber ( int permutationNumber , int geneNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int generatePermutationNumberCellLineNumberorGeneSetNumber ( int permutationNumber , int cellLineNumberorGeneSetNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long generateMixedNumber ( int permutationNumber , int elementTypeNumber , int elementNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long generateMixedNumber ( int permutationNumber , short elementNumber , short cellLineNumber , int geneSetNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long generateMixedNumber ( int permutationNumber , short elementNumber , short cellLineNumber , short geneSetNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int generateElementNumberCellLineNumber ( int elementNumber , int cellLineNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long generateLongElementNumberCellLineNumberKeggPathwayNumber ( int elementNumber , int cellLineNumber , int keggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int generateElementNumberCellLineNumberKeggPathwayNumber ( short elementNumber , short cellLineNumber , short keggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long removeCellLineNumber ( long permutationNumberElementNumberCellLineNumberKeggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long addKeggPathwayNumber ( int elementNumberCellLineNumber , int keggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { long elementNumberCellLineNumberKeggPathwayNumber = Long . MIN_VALUE ; switch ( generatedMixedNumberDescriptionOrderLength ) { case LONG_5DIGITS_ELEMENTNUMBER_5DIGITS_CELLLINENUMBER_5DIGITS_KEGGPATHWAYNUMBER : <START_BUG> elementNumberCellLineNumberKeggPathwayNumber = ( elementNumberCellLineNumber * 100000 ) + keggPathwayNumber ; <END_BUG> break ; default : break ; } return elementNumberCellLineNumberKeggPathwayNumber ; } public static long addKeggPathwayNumber ( long permutationNumberElementNumberCellLineNumber , int keggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static int removeCellLineNumberAddKeggPathwayNumber ( int mixedNumber , int keggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public static long removeCellLineNumberAddKeggPathwayNumber ( long mixedNumber , int keggPathwayNumber , GeneratedMixedNumberDescriptionOrderLength generatedMixedNumberDescriptionOrderLength ) { } public void findAllOverlappingDnaseIntervalsWithoutIOWithNumbersForAllChromosomes ( int permutationNumber , IntervalTreeNode node , InputLineMinimal interval , ChromosomeName chromName , TIntIntMap dnaseCellLineName2ZeroorOneMap , int overlapDefinition ) { } public void findAllOverlappingTForHistoneIntervalsWithoutIOWithNumbers ( IntervalTreeNode node , InputLineMinimal interval , ChromosomeName chromName , TIntByteMap tforHistoneNumberCellLineNumber2PermutationZeroorOneMap , int overlapDefinition ) { } public void findAllOverlappingDnaseIntervalsWithoutIOWithNumbers ( int permutationNumber , IntervalTreeNode node , InputLineMinimal interval , ChromosomeName chromName , TIntByteMap dnaseCellLineNumber2PermutationZeroorOneMap , int overlapDefinition ) { } public void findAllOverlappingDnaseIntervalsWithoutIOWithNumbers ( int permutationNumber , IntervalTreeNode node , InputLineMinimal interval , ChromosomeName chromName , TIntIntMap permutationNumberDnaseCellLineName2ZeroorOneMap , int overlapDefinition ) { } public void findAllOverlappingDnaseIntervalsWithNumbersStringBuilder ( String outputFolder , WriteElementBasedAnnotationFoundOverlapsMode writeElementBasedAnnotationFoundOverlapsMode , IntervalTreeNode node , Interval interval , ChromosomeName chromName , byte [ ] oneOrZeroByteArray , int overlapDefinition , TShortObjectMap < StringBuilder > cellLineNumber2CellLineNameMap , TShortObjectMap < StringBuilder > fileNumber2FileNameMap ) { } public void findAllOverlappingDnaseIntervalsWithNumbers ( String outputFolder , WriteElementBasedAnnotationFoundOverlapsMode writeElementBasedAnnotationFoundOverlapsMode , IntervalTreeNode node , Interval interval , ChromosomeName chromName , byte [ ] oneOrZeroByteArray , int overlapDefinition , TShortObjectMap < CharSequence > cellLineNumber2CellLineNameMap , TShortObjectMap < CharSequence > fileNumber2FileNameMap ) { } public void findAllOverlappingDnaseIntervalsWithNumbers ( String outputFolder , WriteElementBasedAnnotationFoundOverlapsMode writeElementBasedAnnotationFoundOverlapsMode , IntervalTreeNode node , Interval interval , ChromosomeName chromName , byte [ ] oneOrZeroByteArray , int overlapDefinition , char [ ] [ ] dnaseCellLineNames , char [ ] [ ] fileNames ) { } public void findAllOverlappingDnaseIntervalsWithNumbers ( String outputFolder , WriteElementBasedAnnotationFoundOverlapsMode writeElementBasedAnnotationFoundOverlapsMode , IntervalTreeNode node , Interval interval , ChromosomeName chromName , TShortByteMap dnaseCellLineNumber2OneorZeroMap , int overlapDefinition , TShortObjectMap < String > cellLineNumber2CellLineNameMap , TShortObjectMap < String > fileNumber2FileNameMap ) { } public void findAllOverlappingDnaseIntervals ( String outputFolder , IntervalTreeNode node , Interval interval , ChromosomeName chromName , Map < String , BufferedWriter > bufferedWriterHashMap , List < String > dnaseCellLineNameList , Map < String , Integer > dnaseCellLine2OneorZeroMap , int overlapDefinition ) { }

Fix:
elementNumberCellLineNumberKeggPathwayNumber = ( elementNumberCellLineNumber * 100000L ) + keggPathwayNumber ;